5BVG

Selenium incorporated nitrogenase MoFe-protein (Av1-Se2B) from A. vinelandii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U7Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	PEG 8000, NaCl, Imidazole/Malate, Sodiumdithionite

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.582	α = 90
b = 130.825	β = 108.85
c = 107.128	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2015-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97918	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	38.76	97.8	0.151	9.5	7.1		256394

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	97.8		0.795	2.3	7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3U7Q	1.6	101.38	243657	12691	96.56	0.15292	0.15156	0.17913	RANDOM	13.776

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.66		0.37	-0.53		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.584
r_sphericity_free	20.813
r_dihedral_angle_4_deg	19.58
r_dihedral_angle_3_deg	12.519
r_dihedral_angle_1_deg	5.969
r_sphericity_bonded	3.236
r_long_range_B_refined	1.781
r_long_range_B_other	1.781
r_angle_refined_deg	1.53
r_angle_other_deg	1.484
r_scangle_other	0.82
r_rigid_bond_restr	0.711
r_mcangle_it	0.696
r_mcangle_other	0.696
r_scbond_it	0.665
r_scbond_other	0.665
r_mcbond_it	0.536
r_mcbond_other	0.536
r_chiral_restr	0.094
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15897
Nucleic Acid Atoms
Solvent Atoms	1433
Heterogen Atoms	145

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
Coot	model building
XDS	data scaling
XDS	data reduction
MOLREP	phasing